2002 Explorer Electrical Problem-Please help

[den327]

I have a 2002 Explorer and a few days ago I went out to start it and it would not start.The battery had juice but not enough to start it.I looked at the sight glass and it was half red and half green.So I tried to charge the battery.It started but barely so I went to advanced auto with the battery.They told me it was reading 9.6V and was probably going bad.I bought a new battery and it started right up.I took the truck out later that day and about an hour after driving the battery light came on and the message center said to check charging system.The voltage guage was also slowly dropping.So now im guessing that the battery was not the problem and went to buy a new alternator.It seems to be charging fine now but the battery light wont go out and the check charging system message is still on.I tried disconnecting the positive and negative battery cables for a minute and they are still on.Does anyone know what could be the problem?
Thank You in Advance.
Dennis

 

[Eneurb]

The charging system is controlled by the Powertrain Control Module. Scan it or have it scanned for codes. Also check central junction box fuse 21.

 

[den327]

I checked for the fuse and there is no fuse in 21.There is only 1 prong in the blank spot so I guess there doesnt need to be one in there.I didnt check the codes yet.The scanner I have borrowed is only good for fords up to 2001.